Multiple sequence alignment - TraesCS7A01G279000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G279000 chr7A 100.000 7949 0 0 1 7949 295220310 295212362 0.000000e+00 14680.0
1 TraesCS7A01G279000 chr7A 86.747 83 2 7 1603 1684 352130403 352130329 5.110000e-12 84.2
2 TraesCS7A01G279000 chr7B 97.067 7127 126 36 846 7949 272743044 272750110 0.000000e+00 11926.0
3 TraesCS7A01G279000 chr7B 90.533 676 62 2 3 677 70535857 70536531 0.000000e+00 893.0
4 TraesCS7A01G279000 chr7B 87.640 89 2 7 1603 1690 662724125 662724205 2.360000e-15 95.3
5 TraesCS7A01G279000 chr7D 94.968 4352 148 35 3625 7949 268840758 268836451 0.000000e+00 6758.0
6 TraesCS7A01G279000 chr7D 96.528 1930 61 4 1698 3622 268842716 268840788 0.000000e+00 3188.0
7 TraesCS7A01G279000 chr7D 95.046 767 20 7 845 1609 268843470 268842720 0.000000e+00 1190.0
8 TraesCS7A01G279000 chr5B 89.924 794 76 3 1 791 537932721 537931929 0.000000e+00 1020.0
9 TraesCS7A01G279000 chr2D 88.287 794 89 4 1 791 497913023 497912231 0.000000e+00 948.0
10 TraesCS7A01G279000 chr2D 96.970 33 0 1 7222 7253 632078134 632078166 4.000000e-03 54.7
11 TraesCS7A01G279000 chr2A 86.792 795 101 4 1 792 102743310 102742517 0.000000e+00 883.0
12 TraesCS7A01G279000 chr2A 96.970 33 0 1 7222 7253 759693232 759693264 4.000000e-03 54.7
13 TraesCS7A01G279000 chr1D 88.000 700 81 3 1 698 439432087 439432785 0.000000e+00 824.0
14 TraesCS7A01G279000 chr3B 84.442 797 114 10 3 794 747092628 747093419 0.000000e+00 776.0
15 TraesCS7A01G279000 chr3B 83.501 794 121 10 3 790 72205021 72205810 0.000000e+00 732.0
16 TraesCS7A01G279000 chr5A 83.479 799 123 9 3 794 14246822 14247618 0.000000e+00 736.0
17 TraesCS7A01G279000 chr5A 83.354 793 123 8 6 791 491580385 491579595 0.000000e+00 725.0
18 TraesCS7A01G279000 chr1B 81.101 799 139 9 3 791 665491689 665492485 5.240000e-176 628.0
19 TraesCS7A01G279000 chr1B 86.420 81 3 6 1611 1690 111909206 111909133 1.840000e-11 82.4
20 TraesCS7A01G279000 chr1A 88.123 261 26 4 7340 7599 554933952 554933696 1.000000e-78 305.0
21 TraesCS7A01G279000 chr6B 84.942 259 27 8 7341 7599 558930713 558930467 1.320000e-62 252.0
22 TraesCS7A01G279000 chr3D 98.148 54 1 0 795 848 597161569 597161516 2.360000e-15 95.3
23 TraesCS7A01G279000 chr3D 84.158 101 10 2 7476 7576 594956998 594957092 8.490000e-15 93.5
24 TraesCS7A01G279000 chrUn 86.517 89 3 7 1603 1690 216508397 216508317 1.100000e-13 89.8
25 TraesCS7A01G279000 chrUn 86.517 89 3 7 1603 1690 398829514 398829594 1.100000e-13 89.8
26 TraesCS7A01G279000 chrUn 86.517 89 3 7 1603 1690 444108833 444108913 1.100000e-13 89.8
27 TraesCS7A01G279000 chr2B 86.517 89 3 7 1603 1690 272612563 272612483 1.100000e-13 89.8
28 TraesCS7A01G279000 chr2B 100.000 29 0 0 7222 7250 775588487 775588459 4.000000e-03 54.7
29 TraesCS7A01G279000 chr5D 84.270 89 5 4 1603 1690 432432981 432433061 2.380000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G279000 chr7A 295212362 295220310 7948 True 14680 14680 100.000 1 7949 1 chr7A.!!$R1 7948
1 TraesCS7A01G279000 chr7B 272743044 272750110 7066 False 11926 11926 97.067 846 7949 1 chr7B.!!$F2 7103
2 TraesCS7A01G279000 chr7B 70535857 70536531 674 False 893 893 90.533 3 677 1 chr7B.!!$F1 674
3 TraesCS7A01G279000 chr7D 268836451 268843470 7019 True 3712 6758 95.514 845 7949 3 chr7D.!!$R1 7104
4 TraesCS7A01G279000 chr5B 537931929 537932721 792 True 1020 1020 89.924 1 791 1 chr5B.!!$R1 790
5 TraesCS7A01G279000 chr2D 497912231 497913023 792 True 948 948 88.287 1 791 1 chr2D.!!$R1 790
6 TraesCS7A01G279000 chr2A 102742517 102743310 793 True 883 883 86.792 1 792 1 chr2A.!!$R1 791
7 TraesCS7A01G279000 chr1D 439432087 439432785 698 False 824 824 88.000 1 698 1 chr1D.!!$F1 697
8 TraesCS7A01G279000 chr3B 747092628 747093419 791 False 776 776 84.442 3 794 1 chr3B.!!$F2 791
9 TraesCS7A01G279000 chr3B 72205021 72205810 789 False 732 732 83.501 3 790 1 chr3B.!!$F1 787
10 TraesCS7A01G279000 chr5A 14246822 14247618 796 False 736 736 83.479 3 794 1 chr5A.!!$F1 791
11 TraesCS7A01G279000 chr5A 491579595 491580385 790 True 725 725 83.354 6 791 1 chr5A.!!$R1 785
12 TraesCS7A01G279000 chr1B 665491689 665492485 796 False 628 628 81.101 3 791 1 chr1B.!!$F1 788

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
276 278 0.179006 GTCCTCAATCAGCATCCCCC 60.179 60.000 0.00 0.0 0.00 5.40 F
653 662 0.320421 TCAGCGGTACTTTGCTCCAC 60.320 55.000 5.09 0.0 40.03 4.02 F
2071 2090 0.250727 TGTTGGGGTTACTCAGCTGC 60.251 55.000 9.47 0.0 0.00 5.25 F
3197 3220 0.595588 TTTTGTGTATGCCAGTGCCG 59.404 50.000 0.00 0.0 36.33 5.69 F
4846 4902 1.741401 CCATCGAAGCGAACTGGCA 60.741 57.895 0.00 0.0 39.99 4.92 F
6151 6218 1.129998 CTGAAGAGCAAGCATCCAACG 59.870 52.381 0.00 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1815 1.363807 GCACTGAGCAAACAACCCC 59.636 57.895 0.0 0.0 44.79 4.95 R
2552 2573 6.071616 GGGTTGCCTCTTTTATGTGAATTGTA 60.072 38.462 0.0 0.0 0.00 2.41 R
3455 3478 1.748493 CTTCCTCTCGTTCTCCTCCAG 59.252 57.143 0.0 0.0 0.00 3.86 R
5053 5109 0.387929 TGAGTGTGGTTCGAGTGGTC 59.612 55.000 0.0 0.0 0.00 4.02 R
6837 6907 0.322456 TGAAAGACAATGGGCGAGGG 60.322 55.000 0.0 0.0 0.00 4.30 R
7843 7924 0.393537 CAGCCCAGCTCCTAACCTTG 60.394 60.000 0.0 0.0 36.40 3.61 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.673033 CCCACGACATTCAGAGGTGTC 60.673 57.143 7.61 7.61 40.94 3.67
84 86 0.249741 CGCCCGAACCCTAATGTAGG 60.250 60.000 0.00 0.00 45.81 3.18
107 109 1.482593 CCTTCATAGAACAGCCGAGGT 59.517 52.381 0.00 0.00 0.00 3.85
119 121 1.365633 CCGAGGTGCTAGCTGGATC 59.634 63.158 17.23 7.88 0.00 3.36
239 241 4.024556 CCATCGAAATCAACAGATGTAGGC 60.025 45.833 0.00 0.00 38.91 3.93
245 247 4.851639 ATCAACAGATGTAGGCTCCTTT 57.148 40.909 0.00 0.00 0.00 3.11
276 278 0.179006 GTCCTCAATCAGCATCCCCC 60.179 60.000 0.00 0.00 0.00 5.40
315 322 2.978010 CACCGTGCACCACCTTCC 60.978 66.667 12.15 0.00 0.00 3.46
401 408 2.031870 ACATGTGCTAGCGACCAGATA 58.968 47.619 10.77 0.00 0.00 1.98
449 456 1.466025 AACTGAAGGTGCGGGTCGTA 61.466 55.000 0.00 0.00 0.00 3.43
521 528 0.669077 CTTCCTCCCCTACGATCACG 59.331 60.000 0.00 0.00 45.75 4.35
653 662 0.320421 TCAGCGGTACTTTGCTCCAC 60.320 55.000 5.09 0.00 40.03 4.02
685 694 1.307976 ACTCCCTCCCCTATCAGCCT 61.308 60.000 0.00 0.00 0.00 4.58
699 708 3.609256 TCAGCCTGATAGGTGATCTCT 57.391 47.619 0.00 0.00 37.80 3.10
707 716 0.339859 TAGGTGATCTCTGCAGGGGT 59.660 55.000 15.13 6.33 0.00 4.95
725 735 3.353836 GCAGCCAGCGGACGAAAA 61.354 61.111 0.00 0.00 0.00 2.29
734 744 2.309326 CGGACGAAAAACCGGTGAA 58.691 52.632 8.52 0.00 44.59 3.18
797 810 5.354842 CCTAAACGAGAGGGTAATTTCCT 57.645 43.478 0.73 0.49 37.33 3.36
798 811 6.475596 CCTAAACGAGAGGGTAATTTCCTA 57.524 41.667 0.73 0.00 34.21 2.94
799 812 7.063934 CCTAAACGAGAGGGTAATTTCCTAT 57.936 40.000 0.73 0.00 34.21 2.57
800 813 6.929606 CCTAAACGAGAGGGTAATTTCCTATG 59.070 42.308 0.73 0.00 34.21 2.23
801 814 6.555463 AAACGAGAGGGTAATTTCCTATGA 57.445 37.500 0.73 0.00 34.21 2.15
802 815 6.749036 AACGAGAGGGTAATTTCCTATGAT 57.251 37.500 0.73 0.00 34.21 2.45
803 816 6.749036 ACGAGAGGGTAATTTCCTATGATT 57.251 37.500 0.73 0.00 34.21 2.57
804 817 6.525629 ACGAGAGGGTAATTTCCTATGATTG 58.474 40.000 0.73 0.00 34.21 2.67
805 818 6.099845 ACGAGAGGGTAATTTCCTATGATTGT 59.900 38.462 0.73 0.00 34.21 2.71
806 819 7.289317 ACGAGAGGGTAATTTCCTATGATTGTA 59.711 37.037 0.73 0.00 34.21 2.41
807 820 7.815068 CGAGAGGGTAATTTCCTATGATTGTAG 59.185 40.741 0.73 0.00 34.21 2.74
808 821 7.454225 AGAGGGTAATTTCCTATGATTGTAGC 58.546 38.462 0.73 0.00 34.21 3.58
809 822 7.293535 AGAGGGTAATTTCCTATGATTGTAGCT 59.706 37.037 0.73 0.00 34.21 3.32
810 823 7.227156 AGGGTAATTTCCTATGATTGTAGCTG 58.773 38.462 0.00 0.00 31.86 4.24
811 824 7.072454 AGGGTAATTTCCTATGATTGTAGCTGA 59.928 37.037 0.00 0.00 31.86 4.26
812 825 7.389053 GGGTAATTTCCTATGATTGTAGCTGAG 59.611 40.741 0.00 0.00 0.00 3.35
813 826 8.150945 GGTAATTTCCTATGATTGTAGCTGAGA 58.849 37.037 0.00 0.00 0.00 3.27
814 827 9.202273 GTAATTTCCTATGATTGTAGCTGAGAG 57.798 37.037 0.00 0.00 0.00 3.20
815 828 4.862902 TCCTATGATTGTAGCTGAGAGC 57.137 45.455 0.00 0.00 42.84 4.09
826 839 1.731720 GCTGAGAGCTGTAACCCTTG 58.268 55.000 0.00 0.00 38.45 3.61
827 840 1.002544 GCTGAGAGCTGTAACCCTTGT 59.997 52.381 0.00 0.00 38.45 3.16
828 841 2.233922 GCTGAGAGCTGTAACCCTTGTA 59.766 50.000 0.00 0.00 38.45 2.41
829 842 3.677424 GCTGAGAGCTGTAACCCTTGTAG 60.677 52.174 0.00 0.00 38.45 2.74
830 843 2.832129 TGAGAGCTGTAACCCTTGTAGG 59.168 50.000 0.00 0.00 34.30 3.18
919 932 0.755686 GGGCTCGAACCATGAGATCT 59.244 55.000 7.26 0.00 35.43 2.75
930 946 4.925861 GAGATCTGGCGGCTGGGC 62.926 72.222 15.75 8.17 42.69 5.36
994 1010 2.430610 GGCAGATCACGCTCCCTCT 61.431 63.158 7.04 0.00 0.00 3.69
1007 1023 2.688214 GCTCCCTCTCCATCTCACACTA 60.688 54.545 0.00 0.00 0.00 2.74
1569 1588 2.032681 AGCTGGGGTTCGAGTTGC 59.967 61.111 0.00 0.00 0.00 4.17
1636 1655 4.508584 GGGAGGGAATAACAACTGGAAACT 60.509 45.833 0.00 0.00 0.00 2.66
1682 1701 2.508526 GCTGAGGAGCAAAAGGAGAAA 58.491 47.619 0.00 0.00 45.46 2.52
1768 1787 2.938756 GCTAACTGCTGATGCTTCTGGT 60.939 50.000 8.29 0.00 40.48 4.00
1796 1815 2.566952 GGAACTTGCATCCCATTTCG 57.433 50.000 0.00 0.00 0.00 3.46
2071 2090 0.250727 TGTTGGGGTTACTCAGCTGC 60.251 55.000 9.47 0.00 0.00 5.25
2552 2573 2.143122 TCGCACTCGCTTTTCTCAATT 58.857 42.857 0.00 0.00 35.30 2.32
2636 2657 0.842030 TGGTTGATCTGGCTGGGTCT 60.842 55.000 0.00 0.00 0.00 3.85
2691 2712 8.848182 AGGTACATTGTACAGTATAGTTAGCTC 58.152 37.037 24.35 5.84 0.00 4.09
3197 3220 0.595588 TTTTGTGTATGCCAGTGCCG 59.404 50.000 0.00 0.00 36.33 5.69
3330 3353 3.309954 CCGACTGAAAGCAGGTATTTAGC 59.690 47.826 0.00 0.00 46.60 3.09
3455 3478 7.715249 TGTACATTCCAAAAGATAGATACCAGC 59.285 37.037 0.00 0.00 0.00 4.85
3466 3489 2.393646 AGATACCAGCTGGAGGAGAAC 58.606 52.381 39.19 19.94 38.94 3.01
3592 3615 9.853177 CCTTAATCATTGAAACTAGACCCTAAT 57.147 33.333 0.00 0.00 0.00 1.73
3623 3674 8.788325 ACTTCAACCAGATATTAACCAGTAAC 57.212 34.615 0.00 0.00 0.00 2.50
3783 3834 6.114187 ACTTCCATGTCTCTGTTCATGTTA 57.886 37.500 0.00 0.00 39.53 2.41
3914 3968 7.201705 GCCACAGAGGTAAATTGTATTTCCTAC 60.202 40.741 0.00 0.00 40.61 3.18
4018 4072 6.799512 ACTCTCAACAACAAAAGAGGATTTG 58.200 36.000 3.55 0.00 44.11 2.32
4253 4307 4.328169 GCTTCACTGCATTCAAAAATAGCC 59.672 41.667 0.00 0.00 0.00 3.93
4759 4815 1.837439 TCACGGGGATATTCTTGCTGT 59.163 47.619 0.00 0.00 0.00 4.40
4846 4902 1.741401 CCATCGAAGCGAACTGGCA 60.741 57.895 0.00 0.00 39.99 4.92
5053 5109 2.229784 GAGGAAACATCCAAGTTGCAGG 59.770 50.000 0.00 0.00 0.00 4.85
5148 5204 3.396260 TCCCCTTTTGTTGACTACTCG 57.604 47.619 0.00 0.00 0.00 4.18
5168 5224 2.475864 CGTTGGCAAAATCATGTTGGTG 59.524 45.455 0.00 0.00 0.00 4.17
5310 5367 1.894756 GCGTGTACCACTTGGGCAA 60.895 57.895 0.00 0.00 42.05 4.52
5340 5397 4.633175 TGTAAGCGACCAATCAAACTACA 58.367 39.130 0.00 0.00 0.00 2.74
5858 5922 6.768861 TCAGTTAGATTTTGGTTTTCTCGGAA 59.231 34.615 0.00 0.00 0.00 4.30
5865 5929 2.073816 TGGTTTTCTCGGAATTCGCTC 58.926 47.619 0.00 0.00 39.05 5.03
5888 5953 8.547069 GCTCTATAGATAGTTCAACTTGCTTTG 58.453 37.037 2.11 0.00 0.00 2.77
5911 5976 3.691118 GCACTCTTCATGCTGGTTTGATA 59.309 43.478 0.00 0.00 40.08 2.15
6030 6097 8.525876 CATGTCTTGTGTTAATCGCATATTTTG 58.474 33.333 0.00 0.00 36.40 2.44
6074 6141 2.846206 TGCTGTCTGGATATTTCAGGGT 59.154 45.455 7.03 0.00 33.36 4.34
6151 6218 1.129998 CTGAAGAGCAAGCATCCAACG 59.870 52.381 0.00 0.00 0.00 4.10
6223 6290 9.230122 TCAACATGACTGCTTATTCAATAAGAA 57.770 29.630 19.66 9.35 43.85 2.52
6253 6320 4.054671 CCCATCTAATCTCGACTTGCTTC 58.945 47.826 0.00 0.00 0.00 3.86
6469 6536 2.125766 AACCGTCCTCTTTCCCCAGC 62.126 60.000 0.00 0.00 0.00 4.85
6597 6665 2.032681 GTCCCGAGCAAAGGCACT 59.967 61.111 0.00 0.00 44.61 4.40
6734 6802 3.248602 GCGACACTCAACTGAGAAACAAT 59.751 43.478 13.61 0.00 44.74 2.71
6775 6843 7.495606 TGTGCAGTGTAATCTTATTAGGACATG 59.504 37.037 0.00 0.00 0.00 3.21
6828 6898 2.163412 GCTATGTTTTGTGGGATGCGAA 59.837 45.455 0.00 0.00 0.00 4.70
6837 6907 4.054780 TGTGGGATGCGAACTATCTTAC 57.945 45.455 0.00 0.00 0.00 2.34
6840 6910 2.633481 GGGATGCGAACTATCTTACCCT 59.367 50.000 0.00 0.00 32.93 4.34
6841 6911 3.306156 GGGATGCGAACTATCTTACCCTC 60.306 52.174 0.00 0.00 32.93 4.30
6842 6912 3.566523 GATGCGAACTATCTTACCCTCG 58.433 50.000 0.00 0.00 0.00 4.63
6871 6942 4.997395 TGTCTTTCACATTCCTGCTAGAAC 59.003 41.667 0.00 0.00 0.00 3.01
6890 6961 8.108782 GCTAGAACGTAGTATCAATTTGTTGTC 58.891 37.037 0.00 0.00 45.00 3.18
6911 6982 1.209261 TGATAATGTGGAGCCGCAGAA 59.791 47.619 8.87 0.00 39.95 3.02
6921 6992 3.133901 TGGAGCCGCAGAATATTCTTGTA 59.866 43.478 15.49 0.00 34.74 2.41
6947 7018 7.502120 AAAATTCTATGATCGGACATTGGAG 57.498 36.000 0.00 0.00 0.00 3.86
7103 7182 2.962421 GGTTAGGTAGAGCTGCATCTCT 59.038 50.000 22.65 22.65 44.88 3.10
7150 7229 2.413142 GGAAGACGGGGTCGACGAT 61.413 63.158 9.92 0.00 37.67 3.73
7504 7583 3.702048 CGGCCGGAAGTGGAAGGA 61.702 66.667 20.10 0.00 0.00 3.36
7780 7860 1.074926 TTGGGCCATTGGGTGTTGT 60.075 52.632 7.26 0.00 36.17 3.32
7781 7861 0.188587 TTGGGCCATTGGGTGTTGTA 59.811 50.000 7.26 0.00 36.17 2.41
7792 7873 3.815809 TGGGTGTTGTAGTCTTTTGGAG 58.184 45.455 0.00 0.00 0.00 3.86
7811 7892 2.303311 GAGGTAGTGGGCTCTTCACTTT 59.697 50.000 1.99 0.00 42.17 2.66
7818 7899 1.528129 GGCTCTTCACTTTCAGTGGG 58.472 55.000 4.09 0.00 45.94 4.61
7820 7901 1.202818 GCTCTTCACTTTCAGTGGGGT 60.203 52.381 4.09 0.00 45.94 4.95
7821 7902 2.498167 CTCTTCACTTTCAGTGGGGTG 58.502 52.381 4.09 0.00 45.94 4.61
7822 7903 1.843851 TCTTCACTTTCAGTGGGGTGT 59.156 47.619 4.09 0.00 45.94 4.16
7823 7904 1.949525 CTTCACTTTCAGTGGGGTGTG 59.050 52.381 4.09 0.00 45.94 3.82
7824 7905 0.916086 TCACTTTCAGTGGGGTGTGT 59.084 50.000 4.09 0.00 45.94 3.72
7825 7906 1.134220 TCACTTTCAGTGGGGTGTGTC 60.134 52.381 4.09 0.00 45.94 3.67
7826 7907 1.134098 CACTTTCAGTGGGGTGTGTCT 60.134 52.381 0.00 0.00 42.35 3.41
7827 7908 1.134098 ACTTTCAGTGGGGTGTGTCTG 60.134 52.381 0.00 0.00 0.00 3.51
7828 7909 1.140852 CTTTCAGTGGGGTGTGTCTGA 59.859 52.381 0.00 0.00 35.54 3.27
7829 7910 1.434188 TTCAGTGGGGTGTGTCTGAT 58.566 50.000 0.00 0.00 36.91 2.90
7830 7911 0.686789 TCAGTGGGGTGTGTCTGATG 59.313 55.000 0.00 0.00 32.95 3.07
7831 7912 0.686789 CAGTGGGGTGTGTCTGATGA 59.313 55.000 0.00 0.00 0.00 2.92
7832 7913 1.280133 CAGTGGGGTGTGTCTGATGAT 59.720 52.381 0.00 0.00 0.00 2.45
7834 7915 1.003580 GTGGGGTGTGTCTGATGATGT 59.996 52.381 0.00 0.00 0.00 3.06
7835 7916 1.003464 TGGGGTGTGTCTGATGATGTG 59.997 52.381 0.00 0.00 0.00 3.21
7836 7917 1.679944 GGGGTGTGTCTGATGATGTGG 60.680 57.143 0.00 0.00 0.00 4.17
7837 7918 1.278985 GGGTGTGTCTGATGATGTGGA 59.721 52.381 0.00 0.00 0.00 4.02
7838 7919 2.290260 GGGTGTGTCTGATGATGTGGAA 60.290 50.000 0.00 0.00 0.00 3.53
7839 7920 3.411446 GGTGTGTCTGATGATGTGGAAA 58.589 45.455 0.00 0.00 0.00 3.13
7841 7922 3.814842 GTGTGTCTGATGATGTGGAAACA 59.185 43.478 0.00 0.00 38.70 2.83
7842 7923 4.456911 GTGTGTCTGATGATGTGGAAACAT 59.543 41.667 0.00 0.00 46.14 2.71
7843 7924 4.696877 TGTGTCTGATGATGTGGAAACATC 59.303 41.667 11.10 11.10 46.14 3.06
7864 7955 1.995626 GGTTAGGAGCTGGGCTGGA 60.996 63.158 0.00 0.00 39.88 3.86
7885 7976 5.703592 TGGAACGCTAACATTTTGTCACTAT 59.296 36.000 0.00 0.00 0.00 2.12
7906 7997 4.754667 GACCCACGAGGAACGGGC 62.755 72.222 0.00 0.00 44.90 6.13
7932 8023 2.685897 CGACTTCTCTCGAGGGAATCTT 59.314 50.000 27.36 14.97 35.58 2.40
7933 8024 3.488384 CGACTTCTCTCGAGGGAATCTTG 60.488 52.174 27.36 17.84 35.58 3.02
7943 8034 3.677424 CGAGGGAATCTTGAGGTTCTGAC 60.677 52.174 4.18 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.128938 TCAACAAACCTTTAACACGGGTG 59.871 43.478 0.00 0.00 33.20 4.61
84 86 2.017752 GGCTGTTCTATGAAGGCGC 58.982 57.895 0.00 0.00 0.00 6.53
107 109 2.169352 GGTGAAAGAGATCCAGCTAGCA 59.831 50.000 18.83 0.00 0.00 3.49
119 121 2.205307 GTATCGGACGGGTGAAAGAG 57.795 55.000 0.00 0.00 0.00 2.85
239 241 4.530875 AGGACTATGATGGCAAAAAGGAG 58.469 43.478 0.00 0.00 0.00 3.69
245 247 5.114764 TGATTGAGGACTATGATGGCAAA 57.885 39.130 0.00 0.00 0.00 3.68
276 278 1.530771 CATGGCTCTTCAGGGGGAG 59.469 63.158 0.00 0.00 0.00 4.30
315 322 1.815003 GTTCTGCCTTGGTGATTGGAG 59.185 52.381 0.00 0.00 0.00 3.86
359 366 2.122056 AAGTACAGGGAGGCGGGT 59.878 61.111 0.00 0.00 0.00 5.28
401 408 3.308053 CGATGTTCGAGTGCATGAAATCT 59.692 43.478 0.00 0.00 43.74 2.40
449 456 0.676466 TGGCGATCGCAAAGGTGAAT 60.676 50.000 38.00 0.00 44.11 2.57
521 528 2.606725 CCAAGATGACGAGCTTGATGAC 59.393 50.000 8.31 0.00 46.65 3.06
653 662 1.038130 AGGGAGTCGGATCGGTTCTG 61.038 60.000 0.00 0.00 0.00 3.02
685 694 2.323599 CCCTGCAGAGATCACCTATCA 58.676 52.381 17.39 0.00 37.03 2.15
691 700 1.451028 GCACCCCTGCAGAGATCAC 60.451 63.158 17.39 0.00 43.62 3.06
707 716 4.617520 TTTCGTCCGCTGGCTGCA 62.618 61.111 16.76 0.00 43.06 4.41
719 729 3.473625 AGAGATTTCACCGGTTTTTCGT 58.526 40.909 2.97 0.00 0.00 3.85
723 733 3.064931 GTCGAGAGATTTCACCGGTTTT 58.935 45.455 2.97 0.00 45.19 2.43
725 735 1.402456 CGTCGAGAGATTTCACCGGTT 60.402 52.381 2.97 0.00 45.19 4.44
792 805 5.605534 GCTCTCAGCTACAATCATAGGAAA 58.394 41.667 0.00 0.00 38.45 3.13
807 820 1.002544 ACAAGGGTTACAGCTCTCAGC 59.997 52.381 0.00 0.00 42.84 4.26
808 821 3.118956 CCTACAAGGGTTACAGCTCTCAG 60.119 52.174 0.00 0.00 0.00 3.35
809 822 2.832129 CCTACAAGGGTTACAGCTCTCA 59.168 50.000 0.00 0.00 0.00 3.27
810 823 3.528597 CCTACAAGGGTTACAGCTCTC 57.471 52.381 0.00 0.00 0.00 3.20
843 856 7.435192 CGCTGGTCTAAAATTCTTTCACTTTTT 59.565 33.333 0.00 0.00 0.00 1.94
844 857 6.918022 CGCTGGTCTAAAATTCTTTCACTTTT 59.082 34.615 0.00 0.00 0.00 2.27
845 858 6.438763 CGCTGGTCTAAAATTCTTTCACTTT 58.561 36.000 0.00 0.00 0.00 2.66
846 859 5.048713 CCGCTGGTCTAAAATTCTTTCACTT 60.049 40.000 0.00 0.00 0.00 3.16
847 860 4.455877 CCGCTGGTCTAAAATTCTTTCACT 59.544 41.667 0.00 0.00 0.00 3.41
848 861 4.379499 CCCGCTGGTCTAAAATTCTTTCAC 60.379 45.833 0.00 0.00 0.00 3.18
849 862 3.756434 CCCGCTGGTCTAAAATTCTTTCA 59.244 43.478 0.00 0.00 0.00 2.69
856 869 1.451387 CGGCCCGCTGGTCTAAAAT 60.451 57.895 0.00 0.00 32.45 1.82
982 998 0.753479 GAGATGGAGAGGGAGCGTGA 60.753 60.000 0.00 0.00 0.00 4.35
994 1010 1.676678 GCCGCCTAGTGTGAGATGGA 61.677 60.000 0.00 0.00 0.00 3.41
1120 1136 3.927552 GATTTCGAAATCTCACCCGTC 57.072 47.619 33.51 13.56 41.18 4.79
1636 1655 6.401047 ACGGAGTATTAGCTATTAGCAACA 57.599 37.500 17.59 1.60 42.10 3.33
1768 1787 2.378038 GATGCAAGTTCCCAGCCAATA 58.622 47.619 0.00 0.00 0.00 1.90
1796 1815 1.363807 GCACTGAGCAAACAACCCC 59.636 57.895 0.00 0.00 44.79 4.95
2071 2090 7.115378 GCAAGAATTTCAACACAAGATACCAAG 59.885 37.037 0.00 0.00 0.00 3.61
2552 2573 6.071616 GGGTTGCCTCTTTTATGTGAATTGTA 60.072 38.462 0.00 0.00 0.00 2.41
2691 2712 3.738791 GCCAAATGAAACAGTAAAACCCG 59.261 43.478 0.00 0.00 0.00 5.28
2768 2789 1.330655 CCTCTCTTGCTCGGCCCTAA 61.331 60.000 0.00 0.00 0.00 2.69
3330 3353 2.422127 ACAAAAGTTGAGTGTGGGTTCG 59.578 45.455 0.00 0.00 0.00 3.95
3455 3478 1.748493 CTTCCTCTCGTTCTCCTCCAG 59.252 57.143 0.00 0.00 0.00 3.86
3466 3489 3.056107 TGTCAAATGGTACCTTCCTCTCG 60.056 47.826 14.36 0.00 0.00 4.04
3592 3615 8.598916 TGGTTAATATCTGGTTGAAGTTACTGA 58.401 33.333 0.00 0.00 0.00 3.41
3623 3674 9.408069 GTATAAAGATACAAGGAATCTACCACG 57.592 37.037 0.00 0.00 38.28 4.94
3885 3939 7.309805 GGAAATACAATTTACCTCTGTGGCTTT 60.310 37.037 0.00 0.00 40.22 3.51
4018 4072 6.015940 CCTTGAGATTATAATGGGCCTGTTTC 60.016 42.308 4.53 0.00 0.00 2.78
4253 4307 4.808364 GCAGCACTTAGTTTATCTCCTCTG 59.192 45.833 0.00 0.00 0.00 3.35
4759 4815 3.593096 CTCAACACATGCTAGAAGCTGA 58.407 45.455 0.00 0.00 42.97 4.26
4846 4902 3.498397 CACGCAATTCCTTAGTGAAGTGT 59.502 43.478 10.66 0.00 41.17 3.55
5053 5109 0.387929 TGAGTGTGGTTCGAGTGGTC 59.612 55.000 0.00 0.00 0.00 4.02
5148 5204 3.465871 ACACCAACATGATTTTGCCAAC 58.534 40.909 0.00 0.00 0.00 3.77
5310 5367 5.837437 TGATTGGTCGCTTACAAACAAATT 58.163 33.333 0.00 0.00 0.00 1.82
5858 5922 7.596995 GCAAGTTGAACTATCTATAGAGCGAAT 59.403 37.037 7.16 0.00 34.50 3.34
5865 5929 7.634522 GCCAAAGCAAGTTGAACTATCTATAG 58.365 38.462 7.16 0.00 39.53 1.31
5888 5953 1.068055 CAAACCAGCATGAAGAGTGCC 60.068 52.381 0.00 0.00 43.50 5.01
6030 6097 4.439253 AGCTAATTAGACCCCCATGTTC 57.561 45.455 16.85 0.00 0.00 3.18
6074 6141 2.223363 TGCTCGTTGTTTTCGATTGCAA 60.223 40.909 0.00 0.00 36.26 4.08
6151 6218 5.099042 TCCTGGAGTATTTCTTTGCTACC 57.901 43.478 0.00 0.00 0.00 3.18
6223 6290 2.896685 CGAGATTAGATGGGGAGCTCTT 59.103 50.000 14.64 0.00 0.00 2.85
6253 6320 1.903404 GGCAAAGGGGGACACACAG 60.903 63.158 0.00 0.00 0.00 3.66
6469 6536 2.107041 TACACACTGGACTTGGGGCG 62.107 60.000 0.00 0.00 0.00 6.13
6597 6665 1.297378 CGCTCGCAACGACTCGATA 60.297 57.895 5.20 0.00 33.98 2.92
6648 6716 3.255888 TCGATTCATAGGGATGGTTCTCG 59.744 47.826 0.00 0.00 33.49 4.04
6828 6898 2.368875 CAATGGGCGAGGGTAAGATAGT 59.631 50.000 0.00 0.00 0.00 2.12
6837 6907 0.322456 TGAAAGACAATGGGCGAGGG 60.322 55.000 0.00 0.00 0.00 4.30
6840 6910 2.198827 ATGTGAAAGACAATGGGCGA 57.801 45.000 0.00 0.00 38.36 5.54
6841 6911 2.415893 GGAATGTGAAAGACAATGGGCG 60.416 50.000 0.00 0.00 38.36 6.13
6842 6912 2.827921 AGGAATGTGAAAGACAATGGGC 59.172 45.455 0.00 0.00 38.36 5.36
6890 6961 1.202568 TCTGCGGCTCCACATTATCAG 60.203 52.381 0.00 0.00 0.00 2.90
6935 7006 1.205655 CTCTCAAGCTCCAATGTCCGA 59.794 52.381 0.00 0.00 0.00 4.55
6936 7007 1.205655 TCTCTCAAGCTCCAATGTCCG 59.794 52.381 0.00 0.00 0.00 4.79
6947 7018 2.933495 TGCAATGCAATCTCTCAAGC 57.067 45.000 5.01 0.00 34.76 4.01
7150 7229 1.810853 CGCATCGACAGCCACATCA 60.811 57.895 6.14 0.00 0.00 3.07
7504 7583 2.770802 CTCATCTCCATGAACCTGTCCT 59.229 50.000 0.00 0.00 38.63 3.85
7780 7860 2.570302 GCCCACTACCTCCAAAAGACTA 59.430 50.000 0.00 0.00 0.00 2.59
7781 7861 1.351350 GCCCACTACCTCCAAAAGACT 59.649 52.381 0.00 0.00 0.00 3.24
7792 7873 2.038557 TGAAAGTGAAGAGCCCACTACC 59.961 50.000 0.00 0.00 43.42 3.18
7811 7892 0.686789 CATCAGACACACCCCACTGA 59.313 55.000 0.00 0.00 42.26 3.41
7818 7899 2.768253 TCCACATCATCAGACACACC 57.232 50.000 0.00 0.00 0.00 4.16
7820 7901 4.084011 TGTTTCCACATCATCAGACACA 57.916 40.909 0.00 0.00 0.00 3.72
7832 7913 4.651778 CTCCTAACCTTGATGTTTCCACA 58.348 43.478 0.00 0.00 37.31 4.17
7834 7915 3.330701 AGCTCCTAACCTTGATGTTTCCA 59.669 43.478 0.00 0.00 0.00 3.53
7835 7916 3.691609 CAGCTCCTAACCTTGATGTTTCC 59.308 47.826 0.00 0.00 0.00 3.13
7836 7917 3.691609 CCAGCTCCTAACCTTGATGTTTC 59.308 47.826 0.00 0.00 0.00 2.78
7837 7918 3.562176 CCCAGCTCCTAACCTTGATGTTT 60.562 47.826 0.00 0.00 0.00 2.83
7838 7919 2.025887 CCCAGCTCCTAACCTTGATGTT 60.026 50.000 0.00 0.00 0.00 2.71
7839 7920 1.561542 CCCAGCTCCTAACCTTGATGT 59.438 52.381 0.00 0.00 0.00 3.06
7841 7922 0.548510 GCCCAGCTCCTAACCTTGAT 59.451 55.000 0.00 0.00 0.00 2.57
7842 7923 0.547712 AGCCCAGCTCCTAACCTTGA 60.548 55.000 0.00 0.00 30.62 3.02
7843 7924 0.393537 CAGCCCAGCTCCTAACCTTG 60.394 60.000 0.00 0.00 36.40 3.61
7850 7941 3.710722 CGTTCCAGCCCAGCTCCT 61.711 66.667 0.00 0.00 36.40 3.69
7864 7955 6.861055 CCAAATAGTGACAAAATGTTAGCGTT 59.139 34.615 0.00 0.00 0.00 4.84
7885 7976 1.070105 CGTTCCTCGTGGGTCCAAA 59.930 57.895 3.23 0.00 36.25 3.28


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.